Mechanism of Binding of Fluoroquinolones to the Quinolone Resistance‐Determining Region of DNA Gyrase: Towards an Understanding of the Molecular Basis of Quinolone Resistance

Madurga, Sergio; Sánchez‐Céspedes, Javier; Belda, Ignasi; Vila, Jordi; Giralt, Ernest

doi:10.1002/cbic.200800041

Cited by 45 publications

(40 citation statements)

References 51 publications

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“…The initial mutations always occurred in the gyrA gene and were rarely lost or reversed. In 4 out of 7 instances it was the well-documented S83L mutation (28,29). For the highest levels of resistance, at least one of the several observed mutations in parC was necessary as well.…”

Section: Resultsmentioning

confidence: 95%

Interaction between Mutations and Regulation of Gene Expression during Development of De Novo Antibiotic Resistance

Händel

Schuurmans

Feng

et al. 2014

Antimicrob Agents Chemother

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bBacteria can become resistant not only by horizontal gene transfer or other forms of exchange of genetic information but also by de novo by adaptation at the gene expression level and through DNA mutations. The interrelationship between changes in gene expression and DNA mutations during acquisition of resistance is not well documented. In addition, it is not known whether the DNA mutations leading to resistance always occur in the same order and whether the final result is always identical. The expression of >4,000 genes in Escherichia coli was compared upon adaptation to amoxicillin, tetracycline, and enrofloxacin. During adaptation, known resistance genes were sequenced for mutations that cause resistance. The order of mutations varied within two sets of strains adapted in parallel to amoxicillin and enrofloxacin, respectively, whereas the buildup of resistance was very similar. No specific mutations were related to the rather modest increase in tetracycline resistance. Ribosome-sensed induction and efflux pump activation initially protected the cell through induction of expression and allowed it to survive low levels of antibiotics. Subsequently, mutations were promoted by the stress-induced SOS response that stimulated modulation of genetic instability, and these mutations resulted in resistance to even higher antibiotic concentrations. The initial adaptation at the expression level enabled a subsequent trial and error search for the optimal mutations. The quantitative adjustment of cellular processes at different levels accelerated the acquisition of antibiotic resistance. The de novo acquisition of resistance against antibiotics is known to be accompanied by certain mutations and differential expression of specific genes (1-5). The "radical-based" theory (6, 7) proposes that bactericidal antibiotics cause cell death by a single mechanism, driven by the accumulation of oxygen radicals in the cells. In that case, the cellular response to sublethal concentrations of antibiotics should be similar even for compounds belonging to different classes of bactericidal drugs, such as beta-lactams or fluoroquinolones. The outcome might differ for bacteriostatic drugs, for example, tetracycline. The radical-based theory, however, is the subject of debate (8). The revelation of a common denominator for the adaptation processes to different antibiotics might illuminate the question of a single mechanism from a different angle.Resistance can easily be induced in Escherichia coli by exposure to stepwise increasing sublethal antibiotic concentrations (9). The effects of the acquisition of resistance to amoxicillin on the overall physiology is a complex set of adaptations at the gene expression level, preventing metabolic costs at the expense of the ecological range (10). After the initial stage, the prolonged exposure to antibiotics modulates the SOS response, leading in turn to mutations that cause resistance (11). The mutations generate more permanent resistance, which remains long after the antibiotic pressure has been ...

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Section: Resultsmentioning

confidence: 95%

Interaction between Mutations and Regulation of Gene Expression during Development of De Novo Antibiotic Resistance

Händel

Schuurmans

Feng

et al. 2014

Antimicrob Agents Chemother

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“…Sup also bears striking homology with many other MFS family putative sulfate permeases from a wide range of bacteria. In addition, given that topA and ssb code for a predicted topoisomerase and single-stranded DNA binding protein, respectively, and that gyrase A and topoisomerase IV are known to interact with fluoroquinolones (20,22), it would be intriguing if the TnAbaR23 topA and/or ssb genes contributed to the unusual ciprofloxacin-associated high-level resistance phenotype observed in mutant strain DCO174 following deletion of TnAbaR23 (details below).…”

Section: Resultsmentioning

confidence: 99%

Deletion of Tn AbaR23 Results in both Expected and Unexpected Antibiogram Changes in a Multidrug-Resistant Acinetobacter baumannii Strain

Kochar

Crosatti

Harrison

et al. 2012

Antimicrob Agents Chemother

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ABSTRACTSince the 2006 discovery of theAcinetobacter baumanniistrain AYE AbaR1 resistance island, similar elements have been reported in numerous members of this species. As AbaR1 is distantly related to Tn7, we have renamed it TnAbaR1. TnAbaRtransposons are known to carry multiple antibiotic resistance- and efflux-associated genes, although none have been experimentally studieden bloc. We deleted the TnAbaRtransposon inA. baumanniiA424, which we have designated TnAbaR23, and characterized independent deletion mutants DCO163 and DCO174. The NotI pulsed-field gel electrophoresis (PFGE) profile of strain DCO174 was consistent with targeted deletion of TnAbaR23alone, but strain DCO163 apparently harbored a second large genomic deletion. Nevertheless, “subtractive amplification” targeting 52 TnAbaRand/or resistance-associated loci yielded identical results for both mutants and highlighted genes lost relative to strain A424. PCR mapping and genome sequencing revealed the entire 48.3-kb sequence of TnAbaR23. Consistent with TnAbaR23carrying two copies ofsul1, both mutants exhibited markedly increased susceptibility to sulfamethoxazole. In contrast, loss oftetAR(A) resulted in only a minor and variable increase in tetracycline susceptibility. Despite not exhibiting a growth handicap, strain DCO163 was more susceptible than strain DCO174 to 9 of 10 antibiotics associated with mutant-to-mutant variation in susceptibility, suggesting impairment of an undefined resistance-associated function. Remarkably, despite all three strains sharing identicalgyrAandparCsequences, the ciprofloxacin MIC of DCO174 was >8-fold that of DCO163 and A424, suggesting a possible paradoxical role for TnAbaR23in promoting sensitivity to ciprofloxacin. This study highlights the importance of experimental scrutiny and challenges the assumption that resistance phenotypes can reliably be predicted from genotypes alone.

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“…This suggests that the stacking interactions are strong enough to bind the ligands, but unable to orient them properly, needing additional anchoring points for a correct docking orientation that is provided by the protein. On the other hand, when the docking is performed on the protein alone, the molecule accommodates on top of residues Ser 79 and Asp 83 as had been observed previously [33]. Taking these observations together with the known experimental results available, it is reasonable to consider that the molecule does not bind to any of the two macromolecules prior to complex formation [34,35].…”

Section: Quinolone Bindingmentioning

confidence: 72%

Molecular Determinants of the Bacterial Resistance to Fluoroquinolones: A Computational Study

Lupala¹,

Gómez-Gutiérrez²,

Pérez

2013

CAD

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Quinolones constitute a large class of antibacterial agents whose action is mediated through the formation of a ternary complex with DNA and either, DNA Gyrase or topoisomerase IV, resulting in the inhibition of DNA replication. In order to get a deeper insight into the features of the complex formation, we carried out docking studies of fifteen diverse quinolones to the cleaved topoisomerase IV-DNA complex. Docking studies were performed using the crystal structures of the cleaved complex with levofloxacin and moxifloxacin (pdb entries 3K9F and 2XKK, respectively) using the GOLD software. Ligands dock in positions similar to those of the crystal structures. Analysis of the results reveals that bound quinolones appear intercalated between the two nucleotides that are involved in the DNA cleavage and exhibit hydrogen bonds with Arg 117 and, the latter mediated though a water molecule. Arg 117 has not been described to be involved in resistance, since it is putatively involved in the enzymatic reaction and its mutation would be lethal for the organism. Mutants of Ser 79 exhibit resistance to quinolones which can be explained by the loss of an important anchoring point. Interestingly, quinolone resistance observed in Asp 83 mutants cannot be explained directly on the basis of the loss of a direct interaction, but could be explained on the basis of its involvement at the entrance of the ligands to their binding pocket since the residue is located at the mouth of the pocket. The results of the present study suggest that the 4-keto and 3-carboxyl groups of the fluoroquinolones bind a Mg 2+ before binding to the cleaved topoisomarase IV-DNA complex and use Asp 83 for entry into the binding pocket. Accordingly, mutations that do not conserve the binding capacity for the quinolone-Mg 2+ complex will prevent the binding of this class of ligands. The results we present here are also compared with the structure of PD0305970 a 2,4-dione active against the Ser 79 and Asp 83 mutants.

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Mechanism of Binding of Fluoroquinolones to the Quinolone Resistance‐Determining Region of DNA Gyrase: Towards an Understanding of the Molecular Basis of Quinolone Resistance

Cited by 45 publications

References 51 publications

Interaction between Mutations and Regulation of Gene Expression during Development of De Novo Antibiotic Resistance

Interaction between Mutations and Regulation of Gene Expression during Development of De Novo Antibiotic Resistance

Deletion of Tn AbaR23 Results in both Expected and Unexpected Antibiogram Changes in a Multidrug-Resistant Acinetobacter baumannii Strain

Molecular Determinants of the Bacterial Resistance to Fluoroquinolones: A Computational Study

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